I don't think you can do this as this is an outstanding feature request which has not been implemented yet - https://jira.atlassian.com/browse/GHS-806
You can specify non-working days via JIRA Administration -> Greenhopper -> Non-working Days (http://confluence.atlassian.com/display/GH038/Configuring+your+GreenHopper+Global+Settings) , but if you specify the number of working days in a week to be 5 in JIRA Administration -> System -> Issue Features -> Time Tracking (http://confluence.atlassian.com/display/JIRA/Configuring+Time+Tracking) then JIRA and therefore Greenhopper will assume that the working week is Monday - Friday.
Might be worth voting on https://jira.atlassian.com/browse/GHS-806 to try and get this feature implemented?
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